Abdulkadir Elmas
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/oppti |
| git_branch: RELEASE_3_14 |
| git_last_commit: 778ee5d |
| git_last_commit_date: 2021-10-26 12:55:45 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:02 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the oppti package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oppti.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1344/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oppti 1.8.0 (landing page) Abdulkadir Elmas
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: oppti |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oppti.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oppti_1.8.0.tar.gz |
| StartedAt: 2022-04-13 00:03:08 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 00:04:39 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 90.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: oppti.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oppti.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oppti_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/oppti.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oppti/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'oppti' version '1.8.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'oppti' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gqplot: no visible binding for global variable 'variable2'
gqplot: no visible binding for global variable 'variable1'
gqplot: no visible binding for global variable 'cupper'
gqplot: no visible binding for global variable 'clower'
markOut: no visible binding for global variable 'data'
per.test: no visible binding for global variable 'oppti.result'
per.test: no visible binding for global variable 'weight'
per.test: no visible binding for global variable '..density..'
Undefined global functions or variables:
..density.. clower cupper data oppti.result variable1 variable2
weight
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'markOut':
markOut
Code: function(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp,
marker.proc.list = NULL, dataset = "", num.omit.fit =
NULL, draw.sc = TRUE, draw.vi = TRUE, conf.int = 0.95,
ylab = "Observed", xlab = "Inferred", cohort.name =
NULL)
Docs: function(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp,
marker.proc.list = NULL, dataset = "", num.omit.fit =
NULL, draw.sc = TRUE, draw.vi = TRUE, conf.int = 0.95,
ylab = "Observed", xlab = "Inferred")
Argument names in code not in docs:
cohort.name
Codoc mismatches from documentation object 'oppti':
oppti
Code: function(data, mad.norm = FALSE, cohort.names = NULL, panel =
"global", panel.markers = NULL, tol.nas = 20, ku = 6,
miss.pstat = 0.4, demo.panels = FALSE, save.data =
FALSE, draw.sc.plots = FALSE, draw.vi.plots = FALSE,
draw.sc.markers = NULL, draw.ou.plots = FALSE,
draw.ou.markers = NULL, permutation.tests = TRUE,
n.per.test = 10, draw.per.test = FALSE,
plot.set.per.test = list(BRCA = c("ERBB2"), CCRCC =
c("ERBB2", "TP53")), verbose = FALSE)
Docs: function(data, mad.norm = FALSE, cohort.names = NULL, panel =
"global", panel.markers = NULL, tol.nas = 20, ku = 6,
miss.pstat = 0.4, demo.panels = FALSE, save.data =
FALSE, draw.sc.plots = FALSE, draw.vi.plots = FALSE,
draw.sc.markers = NULL, draw.ou.plots = FALSE,
draw.ou.markers = NULL, verbose = FALSE)
Argument names in code not in docs:
permutation.tests n.per.test draw.per.test plot.set.per.test
Mismatches in argument names:
Position: 16 Code: permutation.tests Docs: verbose
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R'
OK
** running tests for arch 'x64' ...
Running 'test.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/oppti.Rcheck/00check.log'
for details.
oppti.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/oppti_1.8.0.tar.gz && rm -rf oppti.buildbin-libdir && mkdir oppti.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oppti.buildbin-libdir oppti_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL oppti_1.8.0.zip && rm oppti_1.8.0.tar.gz oppti_1.8.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 76128 100 76128 0 0 148k 0 --:--:-- --:--:-- --:--:-- 148k
100 76128 100 76128 0 0 148k 0 --:--:-- --:--:-- --:--:-- 148k
install for i386
* installing *source* package 'oppti' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'oppti'
finding HTML links ... done
artImpute html
clusterData html
dropMarkers html
dysReg html
markOut html
oppti html
outScores html
plotDen html
rankPerOut html
statTest html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'oppti' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oppti' as oppti_1.8.0.zip
* DONE (oppti)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'oppti' successfully unpacked and MD5 sums checked
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oppti.Rcheck/tests_i386/test.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > proc.time() user system elapsed 0.21 0.09 0.28 |
oppti.Rcheck/tests_x64/test.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > proc.time() user system elapsed 0.26 0.01 0.26 |
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oppti.Rcheck/examples_i386/oppti-Ex.timings
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oppti.Rcheck/examples_x64/oppti-Ex.timings
|